rooting and pseudotime calculation need some work

[zouter]

• Pseudotime for cycles doesn't make any sense, because the non-directed geodesic distances are used

• calculate_pseudotime shouldn't just root the trajectory as it sees fit. The rooting should be done before pseudotime calculation/plotting.

Otherwise, you get things like this:

[rcannood]

Adding a small reproducible example ;) In both rootings, things are going wrong.

Example code

library(tidyverse)
library(dyno)

milestone_ids <- c("W", "X", "Y", "Z", "A", "B", "C")

milestone_network <- tribble(
  ~from, ~to, ~length, ~directed,
  "W", "X", 2, TRUE,
  "X", "Y", 4, TRUE,
  "Y", "W", 3, TRUE,
  "Y", "Z", 2, TRUE,
  "A", "B", 1, TRUE,
  "C", "A", 1, TRUE
)

progressions <- 
  milestone_network %>% 
  rowwise() %>% 
  do({
    df <- .
    tibble(
      cell_id = paste0(df$from, df$to, seq_len(20)),
      from = df$from,
      to = df$to,
      percentage = seq(0, 1, length.out = length(cell_id))
    )
  }) %>% 
  ungroup()

trajectory <- wrap_data(
  id = "test",
  cell_ids = unique(progressions$cell_id)
) %>% add_trajectory(
  milestone_ids = milestone_ids,
  milestone_network = milestone_network,
  progressions = progressions
)
g1 <- plot_graph(trajectory, label_milestones = TRUE)
t2 <- trajectory %>% add_root(root_milestone_id = "W")
g2 <- 
  plot_graph(
    t2, "pseudotime",
    pseudotime = calculate_pseudotime(t2), 
    label_milestones = TRUE
  ) + labs(title = "Root W")
t3 <- trajectory %>% add_root(root_milestone_id = "Z")
g3 <- 
  plot_graph(
    t3, "pseudotime",
    pseudotime = calculate_pseudotime(t3), 
    label_milestones = TRUE
  ) + labs(title = "Root Z")

patchwork::wrap_plots(g1, g2, g3)
ggsave("~/plot.png", width = 12, height = 4)

[zouter]

Okay, I understand. So if you root at Y (or W, X), you only want to Z-Y if necessary, but not the other edges. So only the edges that are not accessible should be swapped